I shoot in aperture priority or in manual, depends on the lens I use, if I use extension tubes I use manual because there is no connection between camera and lens. My flower set up is usually like this.

80-200mm F4.5 - I use aperture priority if I shoot wide open or manual if I step down because it is manual lens.

50mm F2 with extension tubes, I use different sizes, depends how close I want to be, in this set up I use manual settings

Now I introduced wide angle lens into my close up photography, which is quite cool, also depends what do you want to get with your images. It is 16-45 F4, here I use aperture priority in 99 percent of the cases.

I never had my camera on auto or program mode. I always choose all settings by myself, I mean if you shoot in AP camera adjusts shutter speed by itself but if I need to tweak something I do it. Sometimes I use spot metering (depends on the color of the flower and the background).

Some of the shots that you can see in this thread I used 35-75mm F3.5-F4.5 (yellow roses to be exact) with extension tubes. I don't use this lens anymore because there are some dust particles inside of the lens that I can't clean. So I had to clean up those photos as you can see in the final images, there is no dust on the flowers.